Geusthaus lodging for Oktoberfest

Try searching for a pension, especially up by the University, or over the river to the southeast.

You can try Booking.com, they have a category for Guesthouses. I briefly looked for late September, there were a few Pensions and Guesthouses listed, but not many, and the prices were no better than a hotel, so I guess my advice would be to not overlook hotels as an option. Using their map option, you can see if the property is close to an S-Bahn, Tram, or Bus line.

You can also consider nearby towns, Freising is nice, Augsburg also works well.

The other caveat I will give, is that obviously room demand is high during Oktoberfest, and looking early is critical...however, if you are a solo traveler, you may find places reluctant to commit to saving a room for you, they may hold out for a double (or maybe you are a couple?).