Looks like a great trip you have planned there. Two suggestions I would throw in for you to consider. Although I have not done this myself, I have heard multiple times that it is much cheaper to rent from Newark NJ than it is from anywhere in NY. Plus you will not have to drive through and out of the city. Might be worth checking out. And the boat trip on the great river - I found that the one in St Paul MN to be much more interesting and enjoyable than the trip from Dubuque.

As for your options of routes.... do you actually have good paper maps or a road atlas to help you plan this trip. All your options are marked on them, and scenic routes are hi-lighted. If you are not able to get them locally, I recommend that you order a Rand McNally atlas, the 2014 edition has been out for a couple of months now. As well as all your electronics, you are going to need good paper maps when on the road. Don't be tempted to rely only on technology.

Lifey