Three days in Israel isn't even enough to scratch the surface. But, if it's all you have, it's all you have.

Jerusalem is, obviously, one of the most fascinating places on the planet, and three days there will give you barely an introduction. I second the recommendation for hiring a guide, or at least taking a walking tour. There's a "free" walking tour (pay what you wish) that meets by Yafo Gate in the Old City - I took it last time I was there, and it was excellent. The Old City is historic and well worth visiting, but it's also a major flashpoint so just be aware of that - the security situation there is something to be aware of. There are all sorts of historic sites and little museums dotted about the Old City, but if you're there for such a short time you won't be able to see all of them. Also, keep in mind that Jerusalem is one place that pretty much shuts down on Shabbat - there are a smattering of places that will be open (mostly in the Arab parts of the Old City, and a few in West Jerusalem), but spending Shabbat in Jerusalem will drastically curtail your sightseeing time.

Tel Aviv is more or less the polar opposite of Jerusalem, and I'd argue that it itself merits well more than three days on its own, too. The city has a wonderful quality of life, an outstanding food and bar scene, beautiful beaches, a gorgeous collection of Bauhaus architecture, old Ottoman buildings, Old Yafo (Jaffa), great shopping... also, the city remains mostly open for business on Shabbat, which is nice.