They are interchangeable and used as intensifiers. The emphasis is in the tone. There is no precise quantification intended or even possible in such a statement.
Note that you would say
We've been doing tons of work.
Not "a tons of work."
Cf. ass ton, shit load, shit ton, etc.
The only way you could establish a ton to mean more than a lot would be to use it in sequence:
Me: Been working hard lately?
You: Yeah, been doing a lot of work.
Me: Really? You seem like you have plenty of time for video games.
You: Dude, I've been doing a ton of work.
But you could easily reverse the two in that exchange and achieve the same effect.