Ummm, if Mr. Colin is OK with the QM2, I don't think I would suggest Freighter travel. LOL!
Bounding the dates to the original desired travel period, you'll arrive in NYC on 16 May and depart back to London on 6 July. That gives you 51 days in the USA. With at least three days on each end of your trip in NYC, you can get away with the 45-day USA Rail Pass, except keep in mind that you will likely travel through blackout dates during major holidays (Memorial Day on last monday of May, and July 4th).
So where do we go from here? 19 May: NY to Niagara Falls, Ontario on the Maple Leaf. You can use your Rail Pass for the trip up to Niagara Falls, NY, then pay for the portion from NY to ON. You arrive in the evening of the 19th. Spend a couple of nights and depart 22 May: From there, you can take VIA Rail on into Toronto (Don't take GO Transit, as it is likely very crowded. Via is an evening departure into the City). Spend a loveley weekend in Toronto. 26 May: I would then recommend taking VIA Rail to Windsor (not part of the rail pass plan, but you would be in Canada during an American holiday/blackout period anyway). It's a four hour trip on an unnamed train. From Windsor, you can take shuttle bus back across the border to Detroit. 28 May: From Detroit, you can take train 353, The midday Wolverine, to Chicago (5 1/2 hours).
1 June: From Chicago, take the Empire Builder to Grand Forks, North Dakota. 2 June: Thank goodness for a very early arrival - you won't need to spend the night here. From Grand Forks, you can take
Winnipeg Grand Forks Shuttle to Winnipeg and back.
5 June: Buggers! You have to now catch the train in Grand Forks at 4:52 AM. Continue on the Empire Builder to Seattle, WA on 6 June. 10 June: From Seattle, take the Coast Starlight to Emeryville and take transit across the bay to San Francisco (now 11 June). 14 June: From San Francisco, I would perhaps take the local commuter train Caltrain to San Jose, catch the Coast Starlight and end up in Los Angeles late that same night.
I think by now you've seen enough of our fabulous mountains (beside, you have those things in Europe). 16 June: I would recommend the Southwest Chief back to Chicago and enjoy some time in the Dessert. Get off the train in Williams, AZ and enjoy a few hours in a cozy motel in town. Either take a tourist train or shuttle to the Grand Canyon on the 17th. Spend a couple of nights there and prepare another cozy couple of hours the night of the 20th and board a van shuttle at 3:30 AM to get back on the Southwest Chief again by 3:50 AM.
Arrive 22 Jun in Chicago. Don't spend a night in Chicago and depart a couple hours later on the Cardinal for some slow winding river hugging through West Virginia. Or spend two nights in Chicago and depart on 24 June. [NOTE: This train only departs Chicago on Tues/Thurs/Sat]
Though this train will get you back into New York the night of the 25th, you still have a week to explore. Add a day or two somewhere along what we've already looked at, and/or spend a couple of days in our Nation's capital in Washington, DC. Finally, on 2 July (don't wait past this, as travel will get very expensive), how about taking the Acela Express - America's TGV, Our Shinkansen, ICE of the West from Washington, DC to New York City.
All in all, this itinerary will work wonderfully for your initial dates of travel, however, you'll be up against a MAJOR holiday weekend up to your departure on the QM2 on 6 Jul. In the Fall, the QM2 schedule will allow you to miss Labor Day in September, make your travels, and be back on board before the Thanksgiving holiday at the end of November. And, the scenery can be much more colorful!