Q: How to acknowledge a contribution of a deceased person? In the acknowledgement section of my thesis, I want to mention a person who is no longer alive.
What is the correct way of saying that?

I want to thank my aunt who assisted me with financially – too pity she cannot see me graduate.  
  I want to thank my aunt who assisted me with financially – your memory will be eternal.  
  I want to thank my aunt who assisted me with financially – too unfortunate she cannot see me graduate.

Or any other version would be appreciated.

A: "I would like to thank my late Aunty for her financial assistance" is brief, and makes the point clearly that she's dead via the word 'late'.
"I want to thank my aunt who assisted me with financially – too unfortunate she cannot see me graduate." That, and the other options sound a bit ridiculous.
You might try:
"I want to thank my late aunt who assisted my financially during my studies"  with:
- and am sad that she will not see me graduate; or
- ,sadly she will not see me graduate.

A: There is no 'correct' way, and in those circumstances the wording needs to be personal, yet still semi-formal.
First, on a minor point, the "with" is incorrect, and using "late aunt" would clearly indicate that she is deceased (thus explaining any subsequent sentiments):

I want to thank my late aunt who assisted me financially.

As I indicated, this has to be a personal choice, but my inclination would be something similar to your middle suggestion, such as:

Her memory will be with me always.
  I will be ever grateful for her assistance.

As regards your other two suggestions, it's not clear from your question whether you have already graduated or whether this thesis is to help you graduate. I don't think it is appropriate to use wording that suggests you have graduated, unless you already have. Also, if you do use this type of wording, the English needs a little correction: the use of "too" is not correct. I would suggest something like:

I am sorry/sad that she cannot ("could not" if it is in the past) see me graduate.

Or even combine the two thoughts:

I will be ever grateful for her assistance, and am sorry that she has not lived to see me graduate.

