Sara is right, there is noise, traffic, and a general hustle of people everywhere, but that's part of the charm of San Jose Centro. For someplace to be comfortable, secure, and close to the museums and pedestrian walkway/Central Mercado I would suggest the Hotel Don Carlos tripadvisor.com/Hotel_Review-g309293-d300214…
with a family friendly old colonial style hotel, good food and delicious (included) breakfast to help you get on your way. Rooms are good size, comfortable beds, hot water as needed and a friendly vibe throughout.
If you have time, take a stroll through the Teatro Nacional with the oldest coffee shop in Central America, it's located in the central square. You might consider an easy walk about with Barrio Bird to see some great architecture (kids enjoy it too) www.toursanjosecostarica.com/index.html Oh, of course Pops Ice Cream for sure!
Have a great trip.