I've never been there, but I think I've heard that the Crayola Experience is a good place for young kids.  I presume it is still on-going.  You can check it out.

As an aside, here is a link to things in PA.  don't know if anything strikes your fancy, or not. 

Hershey Park has a huge reputation.  However, it might not be the best place to take younger kids.  (For one thing, it is a bit pricey.)  Maybe, as an alternative, check out Knoble's Theme Park.  From what I hear, it is a good place to take young kids.  Again, I've never been there, so I can't speak from experience.

Link to Factory tours in PA.  Check them out.    In particular:

There is a listing for Hershey Chocolate.  This is not a "factory tour" per se, but is educational about making chocolate.

I see Kreider Farms in Manheim listed.  That might be an interesting tour to do, especially if your kids do not have (much) exposure to dairy farms, or even if they do.

The other tour you might want to put on your list - for yourself - is the New Holland plant in New Holland, PA. 

I believe there are specific times for this tour, and you will need to make reservations in advance.  (Probably true for most all tours listed.)