With a 3 year old, I would not follow a set schedule. I went to DLR in mid-November with a 3 and 5 year old, and it was ultimately easiest (for us, but your family might be different) to know where we wanted to start the day and if there were any timed events we wanted to do (e.g., see a show or the parades). Then the rest of the day was fluid; we did whatever caught our (i.e., the kid's) eyes. I would always recommend going with the flow because you never know who you'll see or what the little ones will want to do.
For example, we were heading from Dumbo to Tea Cups, but along the way, we saw Captain Hook meeting guests, so we headed over there instead. By being fluid, we also didn't have to worry if we stayed in one place for a while (e.g., the kid's spent two hours on Tom Sawyer's Island, which we figured we'd be done within about 45 minutes). We didn't have a schedule to meet, so it was fine to stay there until the kids were done.
With 5-days in the parks, I think you have enough time to do most of what you want without having to follow a regimented schedule.
