I currently live in Bali and have been to both Komodo and Nusa Penida on dive trips. Admittedly I've only been the once to Komodo. My opinion might not be based on the most experience....
Honestly I think you will be happy with either destination. For me, in order to see Mantas, diving Manta point in NP is a little easier as it's still part of the Bali province and less headache to get to, especially at the moment. NP also has Mola-mola too (not sure if Komodo does?). On my particular trip to Komodo I found the Mantas to seem a little bigger than the ones I saw after in NP - however I'm pretty sure they are both reef manta species and probably the same size (just my mind playing tricks)
Manta bay in NP - I've never seen any mantas there, and the dive shops tell me there hasn't been any for a long time now, so not sure about that one.
On rare occasion (very rare) we get Manta ray passing by here in Amed (Bali), and tech diver friends see Mola-mola quite often here at depths beyond 50m.
Honestly I think you will be happy with either destination. For me, in order to see Mantas, diving Manta point in NP is a little easier as it's still part of the Bali province and less headache to get to, especially at the moment. NP also has Mola-mola too (not sure if Komodo does?). On my particular trip to Komodo I found the Mantas to seem a little bigger than the ones I saw after in NP - however I'm pretty sure they are both reef manta species and probably the same size (just my mind playing tricks)
Manta bay in NP - I've never seen any mantas there, and the dive shops tell me there hasn't been any for a long time now, so not sure about that one.
On rare occasion (very rare) we get Manta ray passing by here in Amed (Bali), and tech diver friends see Mola-mola quite often here at depths beyond 50m.