Well, there's good news and bad news there. The good news is that you should probably have no problem making a Power Pad game. I don't know exactly how the Power Pad works, but it's most likely that it's functionally identical (software wise, anyway) to a regular controller.
Unfortunately the NES Zapper is way more complicated, and requires special programming to get the timing down to the scanline level in order to tell the game where the zapper is pointing, something I doubt will be covered in NESmaker anytime soon. You might be able to do something clever, though, like Super Russian Roulette, though. In that game, the zapper doesn't need to communicate with what's on the screen, it just needs the sensor in the front covered so that it doesn't need light. You don't even have to hold it to your head, you can cover it with your hand or something. Though, I think in that game you can shoot the character on screen, and that DOES require the special programming I mentioned earlier.
Here's some details on the power pad that I found, it looks like it's not identical to a controller, but it's pretty close, and if you're really dedicated to making a game for it, I don't see why you wouldn't be able to tweak the input code to work with it if you're not afraid to get into some ASM programming.
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