All of the available evidence appears to suggest that Miss Havisham is indeed Pip's benefactor. For one thing, she's incredibly rich, and Pip doesn't know anyone else with enough money to be able to make such a generous bequest. Pip comes from a very humble background, and Miss Havisham is the only person he's ever met who could be classed as wealthy. So it's not surprising that he should think that the eccentric old lady is his benefactor.

It's also notable that Pip is informed of his sudden good fortune by Jaggers, Miss Havisham's attorney. Pip has seen him on a number of occasions at Satis House, so when Jaggers pays Pip a visit to tell him about his "great expectations," Pip immediately jumps to the conclusion that Miss Havisham must have something to do with it.

Why did Pip think that Miss Havisham was his benefactor?

For Pip, who is summoned to "play" at Satis House very early on in the novel, Miss Havisham seems to be the only person who could possibly be his benefactor for various reasons.  Primarily, Pip is made aware of his commonness by Estella, the beautiful girl who lives with Miss Havisham and with whom Pip thinks he's in love.  Pip's obsession with Estella continues for the entire novel, and when it comes time for Pip to leave for London so that he can become a gentleman, he assumes Miss Havisham is the one behind it.  (Obviously, as Estella took pride in pointing out that Pip was beneath her with regard to social class, and because he will become educated in London, there seems to be an obvious connection.)

Further, Miss Havisham's wealth is no secret to anyone who lives near her.  Because Pip is raised with Joe and Mrs. Joe, who have very little money, and because the people with whom they're acquainted also have very little money, Miss Havisham again seems to be the only person Pip knows who is financially capable of funding Pip's education.