Munich lodging with car - recommendations?

Look at Hotel Metropol near the train station. They offer cheap parking. It’s very easy to get to, just off the 2R a few blocks. The location is great, rooms are great, breakfast is fabulous.
https://www.hotelmetropol.de/en/offers/

I will happily recommend staying in - or near - the town of Diessen (Dießen) on Ammersee Lake.

Diessen is near Andechs Monastery, which is one of Rick's favorite spots outside Munich.

https://blog.ricksteves.com/blog/face-down-in-my-knuckle-of-pork/

We liked it very much as well. We took Rick's suggested hike from Herrsching (also on Ammersee Lake) to the monastery... lovely, with nice views of the countryside. You can find Diessen, Andechs and Herrsching on this map:

https://media.schneemenschen.de/image/db/2638.jpg

On my first visit to Andechs, we took the train from Munich to Herrsching per Rick's instructions for the hike to Andechs. On a second trip to the area, I had a hotel room in Diessen, and drove the short distance to Andechs. I enjoyed the Diessen's scenic setting and quiet atmosphere a lot.

Now AFAIK, Rick recommends Andechs as a day trip from Munich. But you want to be on the outskirts. So why not stay in the Andechs area and day trip in the reverse direction? Day tripping into Munich should be quite easy from a Diessen base; you could either...

1) ...drive over to Herrsching and ride the S-bahn directly into the city, or...
2) ... catch one of the Ammersee boats over to Herrsching, then ride the S-bahn:

https://www.seenschifffahrt.de/en/ammersee/timetable/timetable/

Diessen is also central to the alpine destinations south of Munich. Füssen, the Wieskirche, and Oberammergau, for example, are only one hour or less from Diessen by car. So it could make really good sense to make an extended stay in Diessen for several days and use it as a base town for all these places. I'd look into an apartment - lots of those in this area.
https://www.booking.com/apartments/city/de/diessen-am-ammersee.html

Check out Hotel Uhland. It's about a .5 to .75 miles from city center. We walked it. They have parking and the rate is low. It is a lovely renovated mansion with a wonderful included breakfast.

If you want to see Munich then stay in a hotel in Munich. The car can be parked in many hotel garages. Consider a hotel downtown and the drive there as a little adventure :-) Or you choose a hotel that is located at a subway station that is not in the middle of the city center. I mean no matter where you stay, in Munich or in the surrounding area, if you want to visit Munich the car just costs money anyway and you will not use it.

Yes I know that goes against the common opinion here but sometimes that's how it is. I've been to Berlin several times with my car and then just parked it in the hotel garage for days.

I second Hotel Uhland. I parked a 9 passenger van in their private parking lot a couple years ago.

Just wanted to add that we usually rent a car, but normally we never drive it into the center of big cities. We had no problems in Munich getting to Hotel Metropol. Wherever you stay, I would recommend using google earth to scout the route in advance so you know what to expect along the way. That makes it so much less stressful.

One thing to be prepared for is that the 2R around Munich is largely underground. So it’s like you are driving through continual tunnels, but with on ramps and off ramps. You come up to the surface every so often, then back underground.

Loved the Andecks Monastery.

Word of caution, the thick dark beer has a very, very high alcohol content. Drink two and you are done. Don't try to drive after drinking the beer.