It is obvious in context that this "whom" refers to both A and B. If you want to highlight a specific person, you will likely need to separate the two a bit in the sentence in order to be understood:
I am thankful to A, and also to B, without whom this project would not have been possible.
[It is also less awkward to use "have been", given that the project is already completed].
In this case, depending on context and delivery, there's a chance that the audience would pick up on B's extraordinary contribution to the project. If you need to get even more explicit, write two separate sentences to make sure that the audience is absolutely certain that A was deserving of your thanks yet somehow completely expendable:
I am thankful to A. I am deeply indebted to B, without whom this project would not have been possible.
Or even:
While I am of of course thankful to A, I will be eternally grateful to B, as without B this project would not have been possible.
So yes, your sentence says what you intend it to convey - with an appropriate delivery, it would never in a million years be interpreted as B singled out for additional praise. If you're still worried about making sure the two are represented equally, a commenter above suggests using "both" to conflate the two people deserving of praise. One interesting non-verbal alternative would be to point at both or otherwise signal the two (maybe tell the two of them to stand up?) as sharing their hard-earned praise.
(But why on Earth would one even need to get so detailed as to show that B was clearly a bigger aid than A? First of all, it's hard to convey this explicitly while being tactful. Most of the time, speakers would just talk about A and B separately, putting a relatively stronger display of thanks on B, and the audience would know from context that B was much more important to the project. Second of all, if you do compare A and B tactlessly, A might be hurt that they were neglected or made to look bad by comparison in their moment of recognition. Usually, if A did something minor to help, one would thank them in a different sentence so as not to lump them in with B or make them look bad compared to B. Imagine how poorly "Thanks A, but B was better" would go over!)