If you want a cheaper option than the hop-on, hop-off bus, you can take the Philly Phlash, a bus that circulates through all the Philly main touristic attractions:
https://ridephillyphlash.com/get-your-passes/
Other tips:
1. Philly is super walkable but you need to drive or take the bus to the Zoo, it's far. Franklin Institute is an easy walk from the regional rail stations at William H. Gray III 30th Street or Suburban Station. All the colonial stuff & Reading Market is near Jefferson Station in Center City/Old City. Under 12 kids ride free on Regional Rail. I would not recommend taking the Philly Metro.
2. Get to Reading Market either right before 11 am for lunch or stroll in around 1 pm, otherwise it will be madness to snag a table.
3. Consider buying a family membership to the Franklin Institute and/or Zoo if you think you can take advantage of the reciprocity programs. With five people it's almost the same price as regular admission.