There are some mistakes with the phrases:
'make a big different' should be 'make a big difference'
This is most common in the past tense, and used to describe someone, instead of saying it directly. "You make a big difference" would not be wrong, but slightly awkward. "You made a big difference to the success of our new client acquisition!".
'make a great accompany' should be 'makes great company'.
It is not wrong to say "You make great company", but it is uncommon. It is much more common to use it when describing someone: "Jess makes great company!" or "Joey is great company!"
[Person's Name], you made a big difference on [some project], thank you!
[Person's Name], thank you so much for your help with [some project]! You are always [some good quality]
John, thank you so much for your help with that report! You are always so helpful.
[Person's Name], it is always a pleasure to work with you! Thank you for your help!
In your question - what are wanting to say would generally be considered too forward in a business or professional setting, at least in the US. In a professional environment, there are generally differences with how genders will be perceived when giving compliments. Men will generally not directly compliment someone else. Instead, it is much more common to thank them for a specific thing they have done. Women will sometimes compliment directly, but I recommend that you do not (regardless of your gender) as it is easy to be misunderstood as flirting.