There is a 3 day deadline to buy bus tickets at a discount. Otherwise it will cost you 66€/person. Best price for the bus with advance purchase (up to 92 days in advance) is as low as 29€/person (58€+ for 2). The sooner you purchase, the lower the price.
The direct train takes a little longer, but you can pre-purchase a Bayern-Ticket online for 27€ (for 2) and use it for the Czech border to Munich. A Czech rail ticket to Germany will cost about 10€/person, so 47€ for two. There are no deadlines for these tickets; you can buy them at that price right up to travel time.
If you know what you are doing, you can purchase a Bayern-Böhmen-Ticket for Pilsen to Munich for 30,50€ from the Bahn Ticket Store and Czech Rail tickets to Pilsen from Czech Rail for about 3,60€/person, 38€ total.
The Bayern- or Bayern-Böhmen-Ticket will also give you unlimited use of the means of transport (S-/U-Bahn, trams, buses) in Munich once you arrive.