There are high chairs available at every WDW restaurant except Victoria & Alberts. However, these would only be appropriate for a child that could sit up unassisted.
If it is possible to leave your stroller outside a restaurant, Disney does encourage you to do so. But if this is not possible because the child is sleeping or something similar, generally you can bring the stroller inside with you. (You can read about an experience of mine with this
HERE.)
With a three month old, where you're going to need the baby held or in the stroller for every meal, my suggestion would be to bring a stroller style which has a removable car seat that clips onto a stroller base. With this, you could unclip the baby's seat from the wheels and just bring that and the baby inside with you. You could put the baby in the seat onto a regular chair or on top of a high chair. This way, the baby is easily visible to you, you're not holding the baby while you're eating, and you're not constantly trying to maneuver the stroller into restaurants.