Michelle, I'm going to beat my friend stanbr to the punch and say YES, cut a night from Santorini and add it to Naxos ..,. Naxos is the deal for families like yours, whereas Santorini is Not. Awful getting around... he's going to be too heavy to carry, and it's a nightmare for strollers (tho do bring a cheap foldable "cane" stroller for Naxos & Athens). The beach towns are on East side of Santorini, black grit beaches, not good for tots ... and pools r no answer for that age. The Famous Caldera View which is the Main THing about santorini is on the West Side requiring tedious (and sometimes crowded) bus ride to access... and if u wd rent car, no place to park!
Your best solution (which vets recommend over & over) is to book a transatlantic nonstop that leaves from East Coast US/Canadian airports, shortest airtime, all arriving (99.9% on time) between 9 - noon... so u can allow 2-hr layover, & catch 1st available domestic flight (Aegean or Sky Express) to Santorini. W luck, u can be in hotel in time to wander a bit & enjoy 7 pm sunset 1st night. Do your main sight-seeing and Caldera-Gazing day 2, and on Day 3 take a ferry to Naxos. There's an AM "rserved-seat" ferry (faster but pricier) arrives Noon-ish at Naxos. At 3:15 pm the BIG Blue Star Conventional ferry (llike small ocean ship - 1200-1800 psgr). It has open rear decks to sit on... arrives 5:30. But can be a hassle going up/down stairs, etc.
For Santorini, think about Hotel near view... but away from hubbub of OIA or FIRA. I favor Firostephani... on N. Fringe of FIra but bypassed by cruise crowds/bus tours. Try to avoid anything w steps DOWN cliff, or UP to higher floors. Sunset Hotel has entry direct off main N-S street, and has large common terrace for sunset views... my own Fave budget pllace, Villa Fotini, has one mainlevel unit w separate bedroom... also check booking.com. W toddler, u will really have to strategize to see stuff!! I advise early on Day #2 book taxi to OIA by 8 am -- you get 2 hrs to wander & take pix before cruise & bus-tour throngs invade.. then you leave, can catch bus to FIRA town for museum, lunch etc. Good Firostephani lunch/dining - Taverna Aktaion, Cafe Remvi/Remvi hotel (great sunset views no crowds sane prices).