Most resorts offer activities for children, the majority have an age limit of five. For a three year old I would suggest contacting The Nanny Connection, most hotels and resorts will refer you to. Do a quick search on the forum for other child care services that have been used by TA'ers.
Boutique style hotels are not many - there are a multitude of condo properties that fit description - perhaps you might like Napili Kai Resort comes to mind - lovely property - Condo's are variable, from basic to luxury - all over, it's very helpful to have extra room with a child. Most of the hotels are big. Hawaii is a familiy destination and there are not a lot of adult oriented properties, as a loose rule of thumb - the smaller the pool, the fewer kids. The time of year has a lot to do with it also. When do you plan to travel? Nightly budget?
Hop over to hawaiirevealed.com/free-travel-info/maui/mau… and look at the properties information, although these are numerous, it is not covering every place. You may see something that you like the look of. Look and see, read reviews here on TA, ask questions.