I will be traveling to Israel in the spring for 8 or 9 days. Mostly I'm interested in historical Jewish sites, and I'd like to get on a tour while there. All of the tourse I've found put the air travel into the trip, but I'd like to arrange my own flights.

What are the best tour companies that provide transportation and tour guides?

You might want to try a private guide for part of the trip.
We were in Israel for a month and used a private guide to visit the North (Golan Heights, etc.) and Masada. He was extremely reasonable ( a lot less expensive than Guides hired in jerusalem) and was fantastic. Extremely knowledgeable and interesting. His name is Arnon and E-Mail address is [email protected]. He is located in Tiberius but will pick you up in Tel Aviv or Jerusalem or elsewhere in israel.
Tell him Ann and jerry recommended him; have a great trip.

We returned just yesterday from 10 days in Israel (our first trip there). We highly recommend Lyana Rotstein, who is a licensed tour guide as well as having an M.A. in Land of Israel Studies. We toured Tel Aviv, Jerusalem, the Galilee, the Golan, and the Dead Sea/Masada and were extremely impressed at the wealth and breadth of her knowledge. Jewish history/sites/traditions, Christian history/sites/traditions, archeology, art, military history---she wowed us with details and explanations. Her email is [email protected] (the first character is a lower-case "L"; the last is the numeral one); phone 972-8-971-4669; cell 972-52-861-0286. Tell her Carla and Frank say hello.

By the way, not to be missed is the newly opened Rabin Museum in Tel Aviv--a gorgeous building that presents all sides of the history of Israel to the present using over 150 film clips as well as photos and print materials. One of the best-designed, most engaging, most user-friendly museums in the world. Enjoy your trip!