Besides the characters of Shylock and Tubal in "The Merchant of Venice", does Shakespeare make any other references to Jews in any of his other plays?

Not in his other plays as I recall, but we mustn't forget about Shylocks daughter, Jessica.

Having now played the part, I can say with certainty that Flute the bellows mender in "A Midsummer Night's Dream" says "Most brisky Juvenal and eke, most lovely Jew".
In "love's Labour's Lost", Costard refers to "my incony Jew" where "incony" means unlearned.

I don't consider Jessica as a particularly Jewish character. From the start Shakespeare already arranges to have her converted, and she does absolutely nothing for the beefit of her Jewish family (in fact she seems all too eager to escape that family).

But as Gmack says here, not all of Shakespeare's refferences to Jews are in such a negative light as Shylock is portrayed.

In "Much Ado About Nothing", towards the end of the second act, Benedick does say of Beatrice, "and if I do not love her, I am a Jew." Kenneth Branagh did well to skip over that line (among others) in his cinematic rendition.

I am sure that somewhere in one of his many plays Shakespeare makes a reference to Jesus.

In "The Merchant of Venice" Shylock sometimes refers to Christians as "Prodigals". Other than that, not really any reference to Jesus. Nor does the word "trinity" ever come up.