I am interested in visiting Lake Baikal and exploring the areas around the lake. What is the best way of doing so and which nearby town should I use as my homebase? I'd expect using a boat to go from the west to the east side is much easier than traveling by land.
As russian, I should mention other firm, much more popular here in Russian:
They have a good set of offers, including Eco projects with volunteer work (linked above), and more traditional tours.
I think you should check the Active tours to Baikal - if they are offering the climbing tour, they definitely can provide a tour with boat :) Even if they don't, you can order the guided tour, and take the boat with you.
Another interesting site is about the ships across the Baikal, with schedule of department (only in Russian).
Good luck with your tours and welcome to Russia.
PS: All of my friends who have visited the Baikal were using their own initiative - order tickets to the Irkutsk, and after that move to the Baikal and camp there in open zones - outdoor tourism is allowed in Russia and very popular from the Soviet times.
If you have a friends inside Russia, try to use this option - its much more cheaper and fun :)
Choose Irkutsk as home base. Travel to Olkhon island and rent a boat from there (cheaper) and/or join some group for a day boat trip. Using a boat to go from the west to the east coast is more exciting and quicker, but not cheaper. Public hydrofoil goes on every Monday in July and August. Departure Olkhon (Khuzir village) at 5pm; arrives Ust-Barguzin three and a half hours later.