We are coming to Japan in April to visit my mother in law in Fujisawa. This year we want to go to Takayama. We can easily rent a car for part of the trip (train most of the way and pick up a car) but we aren't sure of a good itinerary--1 day in Takayama and then??? Ideally we would love to rent a house like we did in Kyoto last year because we are traveling with 11 year old twins and a 90 year old mother in law! Yikes big spread. So if the place we stay is nice enough (without be super luxurious because we can't afford it), my MIL could sit and enjoy the place for part of the day if we are doing an activity too strenuous. Any thoughts?

It depends on what you want to see and experience, but I would recommend AT LEAST 1.5 days in Takayama
http://www.japan-guide.com/e/e5900.html

You might want to consider Kanazawa, too. I recommend at least 2 days there, but again, it depends on your interests.
http://www.japan-guide.com/e/e2167.html

thank you. I had not thought of Kanazawa. Also trying to figure out preferably a house/apartment to rent and wondering about the weather in April. Still snow and cold? (that will determine how long we stay!)

I understand that you want to travel out from Fujisawa but you did not mention for how long.

If you are thinking about several days in the Hida region based in Takayama then you have some nice options. West of Takayama is the World Heritage site of Ogimachi, Shirakawgo and nearby is Gokayama (I haven't visited there but think of it is a less-touristed version of Shirakawago.

South of Takayama is Gero Onsen. To the east is Hirayu Onsen and, a bit further, Kamikochi. North of Takayama is Hida-Furukawa (also I have not visited there but understand it to be a smaller and less-touristed version of Takayama).

One visit I made to Takayama was in April for the spring festival. You might want to plan for, or around, it. It was a bit cold and rainy and the cherry trees were still in buds.

I guess it depends on the accommodations and if my mother in law comes. Probably just 3-4 days. Still trying to find a house/apartment to rent as that would work probably best.