Good Hotel near Viktualienmarkt or other location near U-Bahn in Munich?

Try the Eden Hotel Wolf, Arnulfstrasse, directly across the street from the main Railroad station and close to all forms of public transportation.
Excellent resaurant as well.

Sadly, they're booked, any other suggestions? We're going to need three rooms total, including one big family room, so we need something reasonable price-wise but still clean and nice. I know that convenience to public transit will increase the cost, of course.
Thanks!

I stayed at the Hotel am Viktualienmarkt and I also stayed right near by the Hotel Blauer Bock. You may want to try that hotel.

Since you are finding many places already booked, try a search on booking.com for hotels with available rooms on your dates. You can filter the results by location. Once you have identified a few, come back here to ask if you want more information, then contact the hotel directly to book.

I stayed at Hotel am Markt, not sure about their accessibility for someone using a scooter. I enjoyed my stay, right at the viktualienmakt and a short walk to the Marienplatz station, highly rated and well reviewed.

We always stay at the Platzl Hotel as it is less than a 5 minute walk to the Marienplatz and the escalator down to the Ubahn. However, it's not a family style hotel but a somewhat pricey super nice hotel. It's the most convenient if you want to be able to walk to and from the hotel a couple of times a day, say to rest after shopping or traveling. We've also stayed at the Falkenturm, a bit further from the Platzl. Smaller, probably family-run but further from the Marienplatz.

We were very happy with the Blauer Bock in 2015. We were there in October when it was cool, but I understand that the hotel is not air conditioned.

http://hotelblauerbock.de/

We had a good stay at the Marriott City Center Hotel which has an entrance directly into the subway station. I think it was 2 stops from the train station.

I would use a hotel search engine. I like HRS.Com. One search criteria is wheel chair accessibility to cover the scooter. The map associated with each hotel will show Ubahn and Sbahn stops. You can sort the hotels by distance from a particular sight like Marienplatz.

convenient to the U-Bahn

Is that really what you want? The U-Bahn is not the only commuter train in Munich. The S-bahn is also underground and runs east-west under Munich. One of the S-bahn stations is at Marienplatz.

Pension Lindner is only a few blocks from Marienplatz and has an elevator, so it might be accessible. It's a convenient location and a good price for Munich.

If you are in Munich between September 16 and October 3 that is the Oktoberfest. Which would explain the hotels being booked. You'll find many hotels raise their rates significantly. Expect large crowds around town even outside the fairgrounds.

Robert raises a good point - perhaps not the best idea to stay in Munich during Oktoberfest unless that's your reason for going.

I've always stayed close to the train station, as it's a short walk to the city center or if you're feeling tired a very short S-bahn or U-Bahn trip depending on where you're going. Hotels are cheap there and while it's not exactly a charming area, you're only in the hotel to sleep, in theory. However with Oma in a scooter I can see the advantage of staying more in the center.

For your needs I'd second the Marriott City. I also remember them making a very nice breakfast, and hand made omelets.