Could someone tell me what Car rental company has the best prices...from downtown close to cruise port
I can't tell you which company has the best prices, but we've always rented from Blue. They have locations at the Keflavik airport and in downtown Reykjavik. You might need to taxi from the cruise port to their location. Lotus is also recommended frequently on various forums. Depending on how far you are planning to drive, you should consider getting all of the insurance offered (sand/wind/ash etc).
We too always rent from Blue. I do not look for the cheapest, I go with the most reputable, which is Blue and Lotus for Iceland. As mentioned, get the full insurances as Iceland is a whole other ballgame!