Can you talk to him about it? my ds is 26 mo and is starting to mention me he's "scared" of some noises (like the trees that plop into the window or the doorbell.. have to agree on this one with him, i also hate it LOL)... i make ds face his fears while awake, listening to different sounds and explaning him that at first i was also scared but then i realized it was just a: dog, cat, car, etc. Lots of practice with it during daytime and it can become a fun game.
You can also mask the outside sounds with a white noise machine or soothing music and ask him if that works better for him.
Talk to him a lot about it and try and get more info about the noise, is it something that is scaring him now? was a loud noise in the past weeks that frightened him and now he's obsessed with it and causes him anxiety? is he doing this because he knows this will bring mommy back to bedroom for playtime? (of course, he won't answer on this one but you can figure out from other answers and behaviour).
If molar pain is making him be upset, the right dosage of meds will help you on this one. Check with your ped. My ds tends to say the weirdest things (That usually have nothing to do with the real thing) whe he's feeling cranky, like go away daddy (and daddy is not even in the house) or i don't want to sing (and we're not singing...) i guess is just out of the frustration and upsseting, that they want to express that something's wrong but don't know how to do that or what to say to get the reaction they're looking for.
Don't minimize his fears or ignore them. Stay an extra 5 mins in the room when putting him down to reassure him. Give extra cuddles... and an earlier bedtime on days he misses a nap. It is also common for them to start skipping naps around the 3 year mark, but offering quiet/down time is just what's adviced... they still need a break in the middle of the day to recover from activities.
Good luck and HTH!