If you're shooting long exposures anyway, then keep the ISO as low as possible which will minimise noise. Shoot at ISO100 and turn the camera's noise reduction ON. Your alternative is to shoot your own dark frame and subtract it later in Photoshop. I'd let the camera do it. The camera will effectively take a second 'dark' exposure after the shutter has closed so you won't see your histogram until it's done that (takes as long as the first exposure), but you can use it for another shot while you're waiting.
For long exposures I set to 'bulb', shoot at ISO100, NR turned on, dark slide over the eyepice, mirror locked up (not critical for longer exposures), using the cable release. On a tripod, of course. Process RAW files in ACR, apply noise reduction in Photoshop using Noise Ninja. If there are any points of light in the scene (distant buildings, etc.) I'll often bracket as it's hard to predict the effect of these in the final image, aso I may end up blending several exposures.
Experiment; go outside tonight and shoot a 2 min exposure with NR on, and one with it off, and see if you feel the noise is acceptable in either method. DPP won't really help you remove the noise you get with NR off, and Noise Ninja etc will soften it too much.