Puerto Vallarta is great. Excellent mix of culture/history with laid back beach life.
I got married there in 2011. Did a fairly affordable all-inclusive resort since we had a number of guests. The resort used our wedding to film a promo -
Get Married at Dreams Villamagna (I'm the groom, not the 20-something dude with abs they used to show off the spa/etc).
I would give it a solid thumbs-up for family vacation but keep in mind that it's one of those resorts that's lined up down the beach with thirty other resorts and it's a cab ride away to do anything "in" Puerto Vallarta.
We stayed in Puerto Vallarta for the honeymoon but switched to
Hacienda San Angel and it was nothing short of amazing. It's a combination luxury resort and art museum with one of the best restaurants in the region. I could talk about that experience at length, but to be honest, it's probably not what you're after when it comes to bringing a 6-yr-old and 4-yr-old with you.
I will say the coolest thing about Hacienda San Angel is that it's NOT a beach resort. It sits higher up the hill in the city so the views are breathtaking. You then walk everywhere which is awesome. (Side note, Puerto Vallarta is built on a steep hill with narrow streets so the cab ride to Hacienda San Angel was an adventure, where you're looking out the windshield thinking "this is it, I'm going to die right here in Mexico.")
Definitely plan a day or half-day around the Malecon. Fun shopping and neat stuff to see (and when you venture inland away from the beach, there are these giant iguanas all over the place, just chilling in the trees).
We did a day-sailing thing around Banderas Bay that was worth the money.
One thing to recognize is that Puerto Vallarta now effectively includes Nuevo Vallarta. The latter is the string of resorts that are all on better beaches (i.e. sandy/pretty) than historical Puerto Vallarta. Best comparison (if you've traveled on the other coast of Mexico) is what Playa del Carmen used to be when compared to Cancun. The beaches in Puerto Vallarta are largely rocky. Not bad, but just different than what you often think of when considering a beach getaway.
I'll stop droning on. You'll have a great time. Good luck!