Estonia has a good rail system, and is connected to Russia and (not directly) to Latvia. If you are coming from Russia, why not take a comfortable overnight train to Tallinn, specially when the Rail station (Balti jaam) is located in front of the Old Town, providing you a beautiful view on arrival.
Estonian rail company, daily trains from Tallinn to St. Petersburg and Moscow. The website (in Estonian and Russian) has timetables and prices, but you can buy tickets only at the rail station. To find good seats, you need to book the tickets in advance (specially if its near weekends or holidays). The train has different seat categories, and prices varies during the seasons, starting at 300 eek (Tallinn - St. Petersburg) or 600 eek (Tallinn - Moscow).
So, with all this options (by Air, Land, or Sea), what is the best way to get to Estonia? Tell us about your experiences in the comments.