If you book in advance and are willing to do a non-refundable booking you can get rates during the week for rooms at Hilton Garden Inn for about $99-160 (I called to ask if the $99 for 2 doubles was still available, it wasn't but she offered a jr. suite for $136). You can stay at the Holiday Inn Midtown with two double beds for about the same price & that includes breakfast, parking is only $25 a day.
If you are planning to visit the Franklin or Drexel, it would save money to join a science museum near your house and take advantage of the reciprocal agreement they have (through ASTC) We did this and can visit our local museum plus those two (and lots more) for only $99.
http://www.astc.org/members/passlist.htm (you may be able to find one for less than $99 in your area).
Also, make sure to put the kids in their swimsuits and visit Sister Cities park, free fun.
Franklin Institute is open select Thurs until 7pm. Place was just about empty from 4-7 when we went. Allowed us to do Drexel first, lunch, then Franklin.
If you want to see Independence Hall, spend the 1.50 each and order your tickets in advance or they may be sold out. (Honestly, younger children aren't going to be interested in the tour, you could walk around the grounds and they would be happier). If you want to go in and see the liberty bell, get there before opening (we skipped the line and looked at it from the outside) The US Mint is free to tour, don't go on a weekend no one is working the floor/machines. Reading Terminal is interesting. Eastern State Penn was really cool but tickets could get pricey, you can't walk from the hotels but parking is free.