I ran Boston in 2021 and considered staying near the start and having a family member drop me off. It's a really bad idea as most of the streets around the start are blocked off, and there aren't hotels in Hopkinton or really anywhere close. I'm not sure exactly how close to the start line you can get by car, and it may result in your wife having to walk a lot farther than if she got dropped off by bus.
That's why you'll want a hotel close to the bus pick-up at Boston Common. Getting to the start line via those busses is logistically the best option for runners. They have that operation down, and it's an efficient and stress free one. I'm not sure where a hotel shuttle would take you; I don't know that any offer shuttles to the start. Whatever shuttle option is available probably takes you to Boston Common.
In terms of watching her, it depends on her pace, but you should be able to see her 2-3 times. You can take the green line on the T to get to Wellesley which is about the halfway point. You can probably see her again at Chestnut Hill, and then make a plan to get to Boylston. Just build in extra time for finding a viewable area on Boylston.