In my experience, the best way to rent in Israel is the through an agent. Someone like Noach Car rental etc....
A few things to make sure of : If you check online for a rate it might not tell you the additional charges. In Israel Liability is Mandatory and they might not tell you until you get to the counter.
Also be careful about driving on Highway 6 (near Tel Aviv that takes you up North). If you don't register your car they will charge you a lot of money. THERE is a phone number you try this number - 972-3-9081100 or in Israel *6116 and press 7.