If the ESB is implemented via MQ Series (is that the same as what's now called Websphere MQ/Websphere Process server?), then you have a software server CI delivering that 'bus' or interface. One option therefore is to create an S/S CI for MQ Series, and place between the source and destination applications.
SApp1 Application CI -> MS Series Software Server CI -> DApp1 for example.
This isn't 100% ideal since the dependency interpretation for an ESB won't be totally correct. i.e. if it's a bus, there will be traffic in both directions. That mean the source and destination apps are both consuming and providing data from/to the SB. However you can probably model that by creating more 'detailed' S/S CIs in the model, since there will likely be message queues for the outbound AND inbound traffic. i.e. model the message queues granularly and it will probably look right. Does that make sense?