One ought to observe that the ancients tended to like both Themistocles and Pericles. But it is true that Pericles has a less marred reputation. Much of this has to do with the ancient historian Thucydides. Thucydides liked Pericles:

For as long as he [Pericles] was at the head of the state during the peace, he pursued a moderate and conservative policy; and in his time its greatness was at its height. When the war broke out, here also he seems to have rightly gauged the power of his country.... Indeed, by his rank, ability, and known integrity, he was enabled to exercise an independent control over the multitude—in short, to lead them instead of being led by them; for as he never sought power by improper means, he was never compelled to flatter them, but, on the contrary, enjoyed so high an estimation that he could afford to anger them by contradiction. Whenever he saw them unseasonably and insolently elated, he would with a word reduce them to alarm; on the other hand, if they fell victims to a panic, he could at once restore them to confidence. In short, what was nominally a democracy became in his hands government by the first citizen (Thuc. 2.65.5-9)

Indeed, Thucydides' interpretation of course of the war revolves around Pericles. Thucydides believes that Pericles' strategy was sound. But after Pericles died in the third year of the war, the men who replaced him as leaders in Athens were incompetent demagogues. These men pursued misguided strategies which squandered the advantages of Athens and ultimately cost her the war. This is not the only way in which one might think of the war. Another view, for example, might emphasize the ways in which Periclean policy seemed designed to goad Sparta into breaking the peace in the first place. But Thucydides' work (and thus his interpretation of Pericles as wise) was highly influential in antiquity and remains highly influential today (his history being by far the best ancient source we have on the war). By comparison, the great historian of the Persian War, Herodotus, admires the cleverness of Themistocles, and advocates strongly for the central role Athens played in defeating the Persians, but his entire narrative is not devoted to Themistocles' importance in the same way.

So the issue of historical reception is important here. Also important is the fact the Pericles dies of disease at the acme of his power, when the issue of the war was still very much in doubt. He did not live to see any setback beyond the ravaging of Attica (though even that nearly undid his career). Nor did he have the face the long denouement of ruling in a post-Peloponnesian War Athens. He is never ostracized, never exiled. Rather than suffering the vicissitudes that Themistocles and many other major Athenian politicians endured, he dies in his prime, leaving a permanent "what if?" question behind him. In the case of Pericles and Themistocles, the Greek admonition to "judge no man happy until his end" seems especially fitting.