See this report comparing Tomcat and Jetty for Comet:
Tomcat tends to have slightly better performance when there are few very busy connections. It has a slight advantage in request latency, which is most apparent when many requests/responses are sent over a few connections without any significant idle time.
Jetty tends to have better scalability when there are many connections with significant idle time, as is the situation for most web sites. Jetty's small memory footprint and advance NIO usage allows a larger number of users per unit of available memory. Also the smaller footprint means that less memory and CPU cache is consumed by the servlet container and more cache is available to speed the execution of non-trivial applications.
Jetty also has better performance with regards to serving static content, as Jetty is able to use advance memory mapped file buffers combined with NIO gather writes to instruct the operating system to send file content at maximum DMA speed without entering user memory space or the JVM.
If your application will have periods where there are idle connections or clients who are simply waiting for a response from the server, then Jetty would be a better choice over Tomcat. An example would include a Stock Market ticker, where the clients are sending few requests and are just waiting for updates.
Additionally, the Jetty team were the pioneers for Comet, and most of the information and examples that I've found tend to focus solely on Jetty. We've used Jetty on a Comet server since 2008 and have been happy with the results.
The other thing to consider is that Jetty is designed as a standalone web server. This means you don't need an Apache server in front of Jetty. We run Jetty standalone on port 80 to serve all of our application's requests, including the Comet requests.
If you use Tomcat for comet requests, you'll most likely need to allow direct access to port 8080 and bypass Apache, as Apache may negate your long polling.