I don't think you will find any Disney excursion which allows babies along. They are very strict about age limitations. Last March we did not do any excursions with DD's ages 3 and 4.
Which cruise are you on? We did the Eastern and did the ports on our own. Some of the excursions can be booked privately to circumvent the age limitation.
Also, you have the option of leaving your little one in Flounders Reef while the rest of the family does an excursion. Some people are not comfortable with that, some are.
Denae