Yes, there are. There is an algorithm that, given any PDA $P$ and any input word $x$, directly checks whether $x$ is accepted by $P$, without first converting $P$ to a CFG. The algorithm takes running time $O(n^3)$ (treating the size of $P$ as a constant that is absorbed into the big-O notation).
The idea is that, given a PDA $P$, we can compute a representation of the set of all possible configurations of the PDA on all possible inputs. This set is traditionally denoted $\text{post}^*(P)$. It is typically an infinite set (thanks to the $\epsilon$-transitions in $P$), but we are rescued by the following beautiful property: $\text{post}^*(P)$ is always a regular language. Therefore, it can be represented by a NFA. Moreover, there is an efficient algorithm to compute a NFA that represents $\text{post}^*(P)$, given $P$.
Now, given an input word $x$, we construct a DFA $D$ that accepts only $x$ and no other word. Then, we use the product construction to construct a PDA $Q$ that accepts an input word iff both $P$ and $D$ accept that word. Next, we compute $\text{post}^*(Q)$ using the aforementioned algorithm. Finally, we check whether $\text{post}^*(Q)$ contains any accepting configuration (i.e., a configuration where both $P$ and $D$ accept); this is straightforward since we have a representation of $\text{post}^*(Q)$ as a NFA.
The theory has been worked out in the model checking community. You can find an overview of the foundations and references where you can learn more, in Section 2.2.2 (Pushdown Systems) of the following survey paper (there are probably many other expositions as well):
Analysis Techniques for Information Security. Anupam Datta, Somesh Jha, Ninghui Li, David Melski, and Thomas Reps. Synthesis Lectures on Information Security, Privacy, and Trust, 2010 April 27, vol 5, no 1, pages 1--164. (access via Springer, Google Books, or Internet Archive)
The resulting algorithm has various nice properties. For instance, if you work through what the construction is doing, you can convert it to an online algorithm that reads one symbol of the input at a time and then updates the set of reachable configurations, in case that is helpful to you. It is possible to view this as a generalization of Tomita's algorithm for GLR parsing, except that Tomita's algorithm only works if the PDA is a LR parser, while the above works for any PDA.