Your question about neighborhoods to stay in Porto and Lisbon depend on your family's ability to navigate steep streets and block out street noise. Baixa, Rossio, Castelo and Alfama in Lisbon are tough for anyone with walking problems. Also those steep streets + basalt sidewalks + any moisture = super slippery. However, I've had a good experience staying in Rossio near the train station - you can cheat the stairs a little by taking the escalators inside Rossio. Also, the train to Sintra leaves out of Rossio. We literally rolled out of our AirBnB and onto the Sintra train in minutes. It's super easy and the train ride is about 1 hr. Much better than trying to find a place to park a rental car in Lisbon and then in Sintra, which is a nightmare for driving with the very tight one-way streets in the historic center.
In Porto, we stayed near the Bolhao area, sort of between Bolhao and Bonfim. It was relatively flat and walking distance to nearly everything on our Porto bucket list - including the food (like Cafe Santiago, Casa Guedes, Tapabento, and most importantly - Mantegaria for the best pasteis de nata).
We did OPO-LIS by train and it was a great journey - so much faster than the hassle of the plane/airport security. We arrived at Santa Apolonia in LIS and cabbed it to our AirBnB. We were three people and found it easier, faster and many times cheaper to take an Uber or MyTaxi (now called FreeNow) than public transit (and I say this as a public transit advocate who never takes cabs/FHV if possible) in both Porto and Lisbon due to the steep elevation, ease, etc. When you Google Maps something, it might look close on a map but note the change in elevation. 900 feet is quite different if at a 35 degree angle especially going up.