The Bonneville would be a really good first 'real' bike. Especially if YOU are the most comfortable on it, and like the looks the most. You've said often you like bikes that look 'like motorcycles' ie. retro standards. The bonnie is really easy to ride, and would be just as at home on the streets of NYC or the curvy roads at Bear Mountain. I think you have the right idea to go for the base model, and then bring it in the thruxton direction. Lower bars, mirrors, and a tach is all you need really. Although a slick 2-1 pipe would really set off the bike.
I say go for the Bonnie, I think it's the bike that you 'want' the most, and your hoping some ones agrees with you.
PS look into frame sliders or case savers, or some sort of tip over damage protection. The NYC streets are a rough place for a bike.