Had to google which ones the WH-1000XM3's are, because theyre awfully similar in name to the WF-1000XM3... Totally not confusing at all Sony!
Over ear vs in ear really is a big debate and up to preference. In air (Airpods Pro in this case) are MUCH more portable. But, the WF-1000XM3's have more battery life and better sound quality (especially with bass, where in ears are just too small to get as much done.) I own both Airpods Pro and WH-1000XM2's, so I can give general advice here, though I have heard that the XM3's have fixed some of the issues I had with the XM2's.
Airpods Pro-
Rated at 4 hours battery life, 3.5 with ANC on, and 3 hours talk time. I find these numbers under-rated for what I get, as I get closer to 5 or 6 hours constant use with Transparency or ANC on. Charge case holds an additional "24 hours", and charges the airpods in ~20 minutes.
Transparency mode (mics bring sound in so that you can hear everything around you) is a GODSEND for people who listen to music while they work such as myself. While sony has this feature, i found it much worse in execution.
BT 5.0 is a nice to have.
I find the ANC actually works better than the Sony's
Auto-pause when the Airpods are removed is another really good nice to have.
Sony WH-1000XM2/XM3
Rated at 30 hours. I call BS. I probably got ~12h on my XM2's, though the XM3's are more power efficient.
I found that they got uncomfortable to wear after a while due to relatively non-breathable materials used on the pads.
Surprise surprise, larger batteries take longer to charge. 3 hours down time if you forget to plug them in.
ANC was overall meh, the headphones has issues blocking things out that my Airpods can.
"Transparency" honestly sucked, the microphones used were so poor that they were easily peaked by my dogs howling. This produced a nauseating amount of audio distortion.
Of course, bulkier. This is a downside to a lot of people.
The app sucks.
Overall I would say Airpods Pro hands down, doubly so if you are an iPhone owner. ESPECIALLY wearing them outside, you dont wanna be that guy stuck in 2006 wearing over-ears in public.