For dense univariate polynomials, the state of the art is due to Kedlaya and Umans (Fast polynomial factorization and modular composition, SIAM J. Comput. 40 (2011), 1767–1802). They obtain randomized algorithms for factoring degree $n$ univariate polynomials over $\mathbb{F}_q$ requiring $O(n^{1.5 + o(1)}\,{\rm log}^{1+o(1)} q+ n^{1 + o(1)}\,{\rm log}^{2+o(1)} q)$ bit operations.
The multivariate case admits a polynomial time reduction to the univariate case. For a good discussion of this and related topics (such as factoring sparse polynomials), see Kaltofen's survey, Polynomial factorization 1987–1991, in Proc. Latin '92, Springer LNCS 583 (1992), 294–313.
I believe that it is still open whether there is a deterministic polynomial time factoring algorithm, although some partial results are known assuming the extended Riemann hypothesis.