Been there 3 times
We went in March and April, Its hot! They run out of water for sale, the lunch included in the tour at the hotel is a buffet and ok. We bought once through Thomas Moore, and once through E-plus. Either way I think you end up using the same or similar bus companies.
You are picked up at your hotel, they take you down to a central location where the ferry leaves for Isla Mujeres to board the bus.
Then they take you to Chichen Itza and provide you with an English speaking guide. Which I highly recommend even if you go on your own.
On the way home they stop at a Mayan village and /or a gift shop. Highly unnecessary as most of the items are for sale at CI or in the hotel district.
Then you have to stop at all the different hotels along the strip to drop every one on the bus off. The entire day is from around 6am till 10pm due to Bus stops.
When we drove we took the toll road out and local back, mainly because we couldn't find the on ramp to the toll road from Valladolid. The check point (to cross the state line) is a little intimidating and the tolls are very high. The difference in cost is negligible between tour and doing it alone given that you need to rent a car and pay the tolls and your entrance admission, lunch and guide at Chichen. If you have a large group or can get one together, I highly recommend a private van.
We also stopped at a Cenote on the way back, which made the entire drive worth it. I might drive again only if I were staying over night.
You can no longer climb the main pyramid (castle) at Chichen, but you can at Coba.
Take a look into a trip to Coba, the drive is easier, as you don't have to cross the state checkpoint, and the tours are shorter.