One answer to your question comes from the paper The Weber-Seifert dodecahedral space is non-HakenThe Weber-Seifert dodecahedral space is non-Haken by Burton, Rubinstein, and Tillmann.
An earlier and "easier" example is (say) the $(1, 2)$-Dehn filling of the figure-eight knot. This manifold is hyperbolic (4.22) and non-Haken (4.41). The references are page numbers in Thurston's lecture notes.
Finally, we We can use SnapPySnapPy to find presentations of the fundamental groups.
Before filling:
In[1]: M = Manifold("4_1")
In[2]: M.fundamental_group()
Out[2]:
Generators:
a,b
Relators:
abbbaBAAB
After filling:
In[3]: M.dehn_fill((1, 2))
In[4]: M.fundamental_group()
Out[4]:
Generators:
a,b
Relators:
abbbaBAAB
abAbaBabAbaBAB
Edit: I remembered that Regina has the Weber-Seifert manifold as one of its examples. So, using the triangulation isomorphism signature, we can import this to SnapPy and find a presentation for its fundamental group. (We can also compute a presentation using Regina - but I prefer the notation for relations used by SnapPy).
In[5]: WS = Manifold("xvLvvvwMvQPPQQQQcehpjtqksntrtvoupwpsuwsvwcgacalvucahatbhapaggjgfk")
In[6]: WS.fundamental_group()
Out[6]:
Generators:
a,b,c,d
Relators:
aDcbcdabdbbc
aDabCADCbc
abdbcdabdACBC
aDBcdaDabbc
In[7]: WS.volume()
Out[7]: 11.1990647408
In[8]: WS.homology()
Out[8]: Z/5 + Z/5 + Z/5
The homology has rank three, so at least three generators are needed. It seems to be open (?) to compute the minimal number of generators.