Craig, there are reasons other than noise involved.
The first is this can you track without error for 4 mins or will your success rate be better with 2 min shots? If you can go with 4 mins then you will get better results with the lower iso, the Canon 20d I use is recommeded to be used at iso1000 - the lower iso seems to give better dynamic range but the major influence on noise is ICNR versus dark frame subtraction. For non-cooled DSLRs ICNR gives better results.
Have a look here also:
http://www.astrosurf.com/buil/eos40d/test.htm