How do I determine which microcontroller can help me measure peak to peak voltages for my 400 kHz sine wave signal?
Well, you could do it the smart way or the boring way.
You are suggesting the ''boring'' way. Nothing wrong with that, the whole SDR world work in this way. You can sample the signal and keep track of the peak of interest, your plan is good. Nyquist helps but it just says that you can reconstruct the wave, not that it's easy to do it.
Assuming a 400 kHz sine wave signal (in books you'll often see cosines for calculus reason but it's the same) sampled at 800 kHz (you could add some iota to the sampling rate to be strict but it doesn't change) you could have two extreme situations:

You sample at the phase point 90° or 270° (π/2 or 3π/2 would be recommended): the sine is at it's peak and you get the perfect, correct answer. Subject to noise and quantization, of course;

You sample at phase 0° and 180°. You sample exactly zero since the sine work that way. But since you know that there's a sine (Nyquist assumes that) you can interpolate a sine in that (Shannon guarantees that)


In the middle you would have some intermediate value but sine interpolation can extract the amplitude (assuming a sine, a periodic 400 kHz signal with another shape has a greater bandwidth limit).
So it can be done in theory, but it's inconvenient at least in practice. Rule of thumb in sampling says that to work comfortably you need about 10 times the frequency as the sampling rate. About 4 Msamples/s, in your case. Actually is not such a great sampling rate since scopes work at some GIGAsample/s but I don't know an AVR with such a converter (last time I've seen them they were at something like 1 Msamples/s).
You could use a DSC (a DSP in controller format) and be happy. The dsPICs for example can do at least 3.5 Msamples/s which could be suitable for job (if you only need the peak). Maybe some C2000 could have a better ADC, they have too many different parts, look in the catalogs.
That was the brute force way. The smart way, if you only need the peak value is to chuck in a diode with a capacitor. This is called an envelope detector (search for it) and it simply charges the capacitor with the highest voltage it sees (less a diode drop, unless you use an active signal rectifier). You can then lazily look at how much there is in the cap. There is some calculation to do since that thing has a response time, or maybe you need a reset transistor to discharge the cap but it's way simpler than sampling the whole signal