I have a membership that covers both. The Chicago Children's Museum leaves the Magic House in the dust. It is easily 6X as large, and we normally spend about 5 hours there, especially in summer when the kids love to splash in the fountains outside.
If your children are VERY young it won't take as long, because several of their usual exhibits are not that great for toddlers, but for older kids prepare to spend time. Mine spend the most time in the fountain room and the foam airplane tower, as well as climbing on that life-size pirate ship. That's not counting any traveling exhibits that might be on.
If you have the $150 Family-level membership at Magic House you will get in free. If you have a SLSC or MOSI membership you will get in for half-price.
PS: Except for the view from the Ferris wheel, the rides on Navy Pier are nothing to write home about; just ordinary carnival-type rides. However, a cruise on the Windy is something else again. It is a tall ship, and on a breezy day going out on that is HUGE fun (well, as long as no one is prone to seasickness.)
http://www.tallshipwindy.com/default2.aspx
If the Windy is out of your budget, at least take a water taxi ride from the Pier. The taxis go either to the Field Museum or to the Willis (Sears) Tower dock, so you can take the water taxi between those two sites.
http://www.shorelinesightseeing.com/watertaximap.html