Actually, with a little careful planning you can get a really mega-science city. Look for a city with a lot of river tiles, and a few hills. The river tiles give an extra trade, and the hills give shields -- for which you use to build wonders. Namely, build Copernicus's Observatory and Newtons University. If you pre-build with a palace, you can almost guarentee yourself getting these.
With a library+university you get a 100% (or is it 125%?) increase in science output from that city. On top of that, both of these wonders double science output, giving you a 700% increase in output from one city.
Also, are you building roads??? I noticed my treasury was low early in one game, and couldn't figure out why. When I noticed I was working tiles with no roads (meaning no trade) the problem became clear! Finally, change governments to either republic or democracy -- both get bonuses to trade, not to mention lower corrruption (meaning you get to actually *use* that trade!). Even going from despotism to monarchy you should net more income due to the lowered corruption.
Cheers,
Shawn