Tel Aviv and Jerusalem are both large cities near the center of the country, which is to say that they are both good choices for you.
Tel Aviv has the advantage of being on the coast, and therefore closer to Haifa, the other large city in the north (away from the Gaza Strip), meaning that it is the better base for visiting Israel alone.
But Jerusalem is closer to Palestine (the non-Gaza part, that is), and is more historic. Based on my "read" of your interests, that could be a slightly better choice for these reason. Tel Aviv would be a close second, in any event, since they aren't that far apart, with the non-central Haifa, a distant third.