It may come as a surprise that the New York bank that last year earned the highest return on average assets is not called Morgan or Citibank or Chemical or Chase, is not located in lower Manhattan's financial district or among the towers of midtown, and is not run by men with Waspish names and conventional banking pedigrees.

The title belongs to Freedom National Bank, a Harlem-based institution whose headquarters is among the storefronts on crowded 125th Street and whose single branch is located in the tough, often-troubled Bedford Stuyvesant section of Brooklyn.

With assets last year of $127 million and deposits of about $82 million, FNB is not a threat to this city's jumbo banks. But its performance in 1981 ranked No. 1 among 46 black-owned banks that are rated in the June issue of Black Enterprise magazine.

Now FNB, perhaps as a measure of its success, has become the subject of a bitterly fought proxy contest among wealthy, self-made black businessmen.

On the one side is the bank's board of directors and the politically powerful Harlem Common Council, a major stockholder in the bank. Challenging that entrenched group for control is Travers J. Bell Jr., 41, a venture capitalist whose brokerage house, Daniels & Bell Inc., is the only black-owned member-firm of the New York Stock Exchange.

Bell, who is the biggest individual FNB shareholder, filed suit last month in U.S. District Court here naming the council and several board members, including FNB president Sharnia Buford. Among the allegations was that the defendants had prevented him from buying a controlling block of stock in the bank so they could use it "for their own personal and private purposes."

"Unwarranted and unsubstantiated," answers defendant Edward Lewis, publisher of Essence magazine and an FNB board member.

"I think desperation is always sickening," says James Dowdy, another FNB board member.

Those are strong words, considering that only a few years ago the only passion stirred by FNB was desperation.

Founded in 1964 by Dodger baseball great Jackie Robinson and several other black businessmen, the bank for years eked out a meager existence financing marginal businesses in Harlem. It operated with a strong social consience and a liberal lending policy, which in 1974 saw losses climb to $1.7 million.

The next year, in a rush to save FNB from bankruptcy, 11 major New York banks and other financial and community institutions recapitalized the bank with $3.7 million. Businessmen were put on the board of directors and a professional management team brought in to run the bank. It was headed by Hughlyn F. Fierce, a Chase vice president who was given a leave by the bigger bank to become FNB's temporary president and chairman.

In essence, FNB reversed its fortunes by acting more like a typical bank and less like a charitable institution. Bad loans were written off, and a large portion of FNB's lending portfolio went to participating with big banks in making loans to major corporations.

Last year more than two-thirds of the bank's $52 million in loans went to established borrowers such as corporations, and the balance to individuals and businesses in Harlem and Bedford Stuyvesant.

"We now lend money with our head, not with our heart," says Buford, who became president of FNB in 1977 after Fierce returned to Chase. As for its 1.16 percent return on average assets, the highest in New York with Morgan Guaranty at 0.75 percent a distant second, Buford says, "Larger banks are not as conservative on lending as we are."

It's a long way from Buford's office on 125th Street to Bell's comfortable downtown office overlooking New York harbor--an appropriate gap considering the differences that separate the two sides in the dispute over control of FNB.

Like the others in the dispute, Bell is a self-made venture capitalist whose holding company, Danbell Group Inc., controls the brokerage firm, a chocolate company, a film production comany, and an investment firm specializing in African ventures, among other things.

In an affidavit filed in federal court, Bell says that he began buying FNB stock in 1974 as an investment and that he never sought control of the bank. Once he gained more than 5 percent, Bell put his father on the bank's board.

A year ago, Bell sought to acquire a block of 10,000 shares of preferred stock, convertible to 25 percent of FNB's common stock, which was held by the Bedford-Stuyvesant Restoration Corp.

Bed-Stuy got the 10,000 shares during the 1975 recapitalization of FNB. However, Bed-Stuy refused to deal with Bell, and in December, FNB filed suit to block Bell, alleging he had made an illegal tender offer. But by the time there was a hearing on the suit, the judge set it aside because a group of board members had already contracted to buy the shares. Ultimately the shares were bought by Harlem Commonwealth Council, whose president Dowdy is an FNB board member.

Calling it an insider deal, Bell, who holds 17 percent of FNB's stock, alleges in his suit that the FNB group unlawfully took control of the stock without proper disclosure to other shareholders.

"This is Bell's final song," says Gerald J. Fields, outside counsel to the bank. "He's got to know it's going nowhere and he's brought it for improper purposes."

The lawyer suggests that Bell's is a nuisance suit, seeking to embarrass FNB into paying premium prices for his FNB shares, for which he paid an average of $10 each.

But Bell denies this, and he repeats the allegation that the board members are using the bank for their own enrichment. "These are a bunch of guys who in the so-called name of the community are out to grab everything they can," says Bell.