Hussein Ibish argues, against the grain, that Marlowe has written the less viciously-anti-Semitic play, in part because he is an equal opportunity offender:
I think the reputation of the Jew of Malta as an anti-Semitic play rests on the absolutely immoral and stereotypically evil character of Barabas and the contrast with the Merchant of Venice and its more nuanced portrayal of Shylock who can be and now usually is portrayed sympathetically. No such sympathetic performance of Barabas is conceivable. However, the key to the Jew of Malta is that none of the other characters are any better -- indeed, all of them prove at least as bad if not worse than Barabas himself. Ithamore, a Turkish Muslim slave purchased by Barabas, proves more vicious, murderous and immoral than his master, although also much less intelligent. The continuously invading Turks have a master plan to turn the entire Maltese population into galley slaves. As for the Christians in the play, I would argue that at every stage they outdo both the Jews and the Muslims in avarice, hypocrisy, violence and sheer unmitigated badness.