Prague to Cesky Krumlov??

I would suggest either Bean or CK Shuttle Service. With 4 days in Prague, you have the time. Or at least its,what I would do.

At about 3 hours each way, it's past my day trip travel threshold. We did really enjoy Cesky Krumlov though. We did a transfer there with CK Shuttle from Prague and then spent a few nights there after spending 3 nights in Prague. Whether or not it's worth it as a day trip is something you'll have to mull over. I like my day trips to be no more than about 1.5 hours each way max. I'll go further if I'm with a private guide in a car and they're touring us around.

We used a private car service in Rick's Eastern Europe book. They hooked us up with a local guide for a few hours, which also helped with booking the only English tour of the Baroque Theater-the ticket agent didn't speak any English at all.

This is also beyond my daytrip distance threshold, but it was a must for me because of the special-interest destination of the Baroque Theater. But there are two other surviving such theaters in Europe - one in Germany and one near Stockholm. It's a very pretty town, but there are other forgotten and preserved towns to see all over Europe. It might be more worthwhile if you have hiking or canoe plans in the same area planned. There are also the Three-T towns, which we didn't have time for. Prague is certainly worth 4 days.

If money is no object go with a tour or by shuttle or private car. Otherwise train or bus. See here: http://www.idos.cz
With just a day trip you spend 6 hours on your way there and back. I recommend to stay overnight. You will enjoy it much more. Crowds of day trippers disappear and Cesky Krumlov at night and early morning - incomparable to the day with its crowds.

We took the CK shuttle from Prague to CK. We did spend the night, which I recommend. But if you can't do that and it's important to you, the shuttle was great. You could take the first one of the day there and the last one to return to Prague.

I would not do a day trip to Cesky Krumlov. In my opinion, it's too far and not worth the time spent. Depending on your interests, you might consider a trip to Terezin with Pavel Batel as your guide. We found it to be very worthwhile and a great addition to our experience in Prague.

Thank everyone for your advice / suggestions. They will all come in handy making our decisions.

We rented a car and drove. Then added a site or two. CK is even better if you spend the night and see after the day trippers go home.
You can see my pics at my personal blog.
http://www.gadtravel.com/2016/10/hungary-tokaj-etyek-budapest-slovakia.html