Sahara Sam's water park is quite close, as is The Funplex. Sesame Place is less than an hour away. You can also check out Macaroni Kid Moorestown or Cherry Hill; there are a lot of very nice playgrounds in the area. South Jersey is very family-friendly, so there's a lot of options.
Before you go to Philly, check out the National Park website to get reserve tickets to visit Independence Hall (a stone's throw from the Liberty Bell); they charge a dollar 'handling fee' each.

Other options include Adventure Aquarium and Cowtown Rodeo (since you mentioned animals and “rural”). If you do Philly, your kids are good ages for the Please Touch Museum and the zoo and Franklin Institute are always good. Hope you have fun!

Bring plenty of water and be prepared for not enough shade. There will be rides/attractions that your whole family can go on. Then, there are a whole bunch of attractions where your 4 and 6 year olds can drive if they are with an adult. Unless they are very tall, they probably won’t be able to go alone. Since you also have a 1 year old. Plan to switch off. Or you all wait in line and then let a couple of people go ahead. Even if diggers aren’t her thing, I expect both your 4 and 6 year olds will love. The one year old will enjoy the playground.

We’re planning a stop at Diggerland on the way home from another destination. From my limited research, there are a lot of campsites and wildlife preserves nearby, so opportunities for nature and hiking.

Diggerland is great. There is a water park nearby.

4 year old son longs to go to Diggerland, so we're going, but what else is there to do in that part of New Jersey? We also have a 6 year old girl (interests: "nature" / animals and fairies / fairytales) and a 1 year old.

Husband is very into history and wants to do a day in Philadelphia (Diggerland is not far from PA border) to see the Liberty Bell, but if there are more rural or lesser known historical sites or museums sort of in Diggerland's vicinity that would be great to know about.