Is the current boiler gas? oil? What do you pay per kwh of electricity vs. how much per therm of gas or gallon of oil?
On the heat strips for my heat pump (on 100A breaker), I used #2 THHN copper (I could have used #3, but the place that I got it from only had #4 and #2 by the foot). Having individual conductors in conduit was easier than trying to fight with larger SE cable (often aluminum). I would probably use THHN or similar, but cable might be cheaper.
Before you go down this road, there are a few things to check:
1. cost of operation. How does electric compare to other sources? How might the price of electricity change in the future compared to other fuels?
2. Can your current electrical service handle an additional 100A load? If it wasn't installed with the assumption that an electric furnance/boiler would be installed, it is probably undersized for the load. You would then need a service upgrade to handle the additional load.
3. There are many types of boilers and you may find something that will ease the chimney issue and installation and not require going to electric
4. This is a good time to look at the size of boiler that is really needed. There are some calculations that can estimate the need, but the more accurate method is to look at how much fuel you used during a heating season along with your location to see what the real heat load is. Your old boiler may have been greatly oversized (often the case) and you may be able to go much smaller (save on initial costs as well as operating costs).