From the looks of my new radiator, the small trans line fitting could be capped with a screw protector I saw at Home Depot. Also, the fat fitting looks like it could be capped with a brass plumbing cap.

What sizes am I looking for?

I have no idea how to cap them, but am curious as to why you want to do it. Do you have a manual tranny?

I have a manual. That is why I would prefer those open holes capped and I know what to use (I think) just have to have the right sizes.

Is the bigger port NPT?

I would stay away from anything in plumbing unless you are willing to use a simple plastic cap that just stays in place after being pushed in. Plumbing threads taper while automotive threads do not. However, you could find a pair of transmission lines at a junk yard and whack off the fittings, then weld up the holes and voila! I did something similar once while plugging egr holes in exhaust head ports of of a Mercedes M110 motor and it still works leak-free.

When using a radiator made for an automatic, with a manual, you dont need to cap anything. The transmission cooler is inside the side tank, but is sealed off from the engine coolant. If the lower fitting bothers you just being there, you can cut it off with a dremel or a saw. Same can be said for the upper fitting.