I just came back and availability is no issue at all, but prices are higher as others reported. Since you're in Shibuya I recommend taking the DT (Den-en-toshi Line) Train down to Tama Station for CHAMP CAMERA at least once. It's only a one hour round-trip journey for about $5 USD transportation cost. They have all the film you can dream of there and C-41 processing can be as fast as 30 minutes (+ qr code scan will take a bit longer).
For convenience, Kitamura Shinjuku West (small location, film processing is first floor) is pretty great. They are right across from MAP Camera Shinjuku, and takes 2-3 hours for C-41 + QR Code scan. Index and CD is optional I think. So you can just drop off your rolls there and browse all the stores and come pick up after.
Price wise:
Just develop C-41 which is base (you can opt for just this): 950yen per roll
Smartphone Transfer (1818x1228 res, 72dpi, 24bit, about 671KB file size): +880yen
High-quality (4358x3023 res, 72dpi, 24bit, about 3-4MB file size): +1100 yen
NOTE: The HQ option STACKS on top of the normal Smart Phone Transfer, so for high quality smartphone you'd pay 1980yen for that + your base 950yen for your develop. I think index was like 100yen or something I forget.
After your rolls are dev/scanned they give you QR code if you opted for the smartphone transfer where you can check and confirm your photos before paying (you pay on pickup, not dropoff).
Some places offer CD which I haven't checked the res yet, probably standard output from whatever fuji or noritsu they use.
For TSA and general travel in asia, take all your film out of the boxes (canisters fine) and put it in a clear ziplock bag labeled "PHOTOGRAPHIC FILM, HAND CHECK ONLY". You can also add an additional label in Japanese or whatever countries language you're visiting and just point to the label to cut through any miscommunication. In some airports, they'll claim anything under 400/800 ISO is fine for the machine. Just ignore it and tell them it's unprocessed rare film and you would appreciate a handcheck. Never had any issues as long as you ask (they did ask to double check my passport when I took 50 rolls through though).