Need a decent hotel near the Coca Cola bus station in Costa Rica
 

I have a friend of mine coming to visit me in Costa Rica on Thursday ( 2 days from now) and we are planing on taking a 6 am bus from San Jose to the Caribbean side Friday at 6 am. We were going to just stay in San Jose that night after eating with my homestay family and I was wondering if anyone knew of a place that is close to the bus station but not actually in the red light district. please help!

No! You don't want the Coca Cola terminal. The Caribbean buses leave from the Gran Terminal del Caribe, several blocks north and east of there. It's still kind of an iffy neighborhood. The Radisson Europa hotel is the closest hotel, but is going to be quite expensive. The cheaper hotels in the neighborhood are going to be questionable.

I have gone out of the Coca Cola terminal twice now and haven't had any problems but that was going to Manuel Antonio both times which not going to lie thought about doing again! But all the buses for the Caribbean side are at a different station?

Yes, the Caribbean Terminal is located somewhere else, the best bet for you is to find a nice hostel in Barrio Amon, which is 10 minutes walk from Caribbean station.
In this area you can find nice, comfortable and clean hostels or small hotels.