The are 6 different ways across 3 unique modes of transportation to help you travel from Köln to MUC. If you're only considering the price, you should check out the train out of Köln towards Marzling, as it is the cheapest to MUC. It's common to find tickets for as low as $53. Train from Köln to MUC, it will get you there soon enough!
On your trip from Köln to MUC, it is best to book as soon as possible. It won't necessarily help reduce your price by a large amount, but will ensure that you have a spot on the bus or train. Shuttle service may be available to MUC. If you're traveling with a large group, you should probably take a shuttle as it will reduce the price per person. Alternatively, there are shared shuttle services available. With this option, you'll want to book as soon as possible to allow the shuttle service enough time to coordinate your pickup and dropoff.