Train and plane flights vary due to demand so it's impossible to give an answer whichever is cheaper. However the most convenient and fastest choice is the train, no doubts. Also when you include luggage fees, tickets to and from the airport, etc. the plane isn't as cheap as it seems...

Unless you're booking really far in advance high-speed train tickets will be expensive. Eurail isn't cheap either including the reservations but it should still be cheaper overall!

Have a look at planners such as DB Navigator and this guide for reservations: https://www.seat61.com/interrail-and-eurail-reservations.htm

London - Amsterdam is around 4h from city center to city center. Unbeatable and thus really popular, book well in advance (35€). More options with a change in Brussels.

Amsterdam - Paris 3h20. Again unbeatable and really popular, book early (32€). There are cheaper but slower options.

Paris - Geneva 3h15. 29€ for the direct train, 10-20€ if you hop off before the border and cross the border on a regional train (30 min longer).

Trains within Switzerland are very frequent and straightforward. Hop on and sit wherever you want. Reservations are not a thing.

Btw boats on Lake Thun and Brienz are fully included in Eurail! 

Interlaken - Venice will take a while but there's some good scenery across the Alps. :)

What would be the travel date for that leg? There are engineering works on the Simplon route until 8th September so I'd suggest the Gotthard route in the meantime (or a 2h replacement bus).