Waterloo Station is where the Eurostar takes off from, yes...
However, I don't see much of a need to stay at a hostel right by Waterloo. Everything is very well connected by the Underground, so I'd choose a hostel based on the price/amenities/proximity to other stuff you want to see. Getting to Waterloo Station in time to catch your train shouldn't be a problem, no matter where you are in London.
If it helps any, Waterloo is on the Jubilee, Bakerloo, and Northern lines. If you want to pick a hostel near any of those, you won't have to make any transfers getting there.