FireLance
Legend
This is how I usually do it:
If the NPC has the mount because of a class feature, the mount is included in the NPC's CR. This makes for some odd cases, like a 1st-level halfling druid mounted on a riding dog, but there is enough of a fudge factor in CR that it doesn't matter very much. If necessary, the DM can include an easier encounter in the same adventure to balance it out.
If the NPC has obtained the mount by spending other resources, e.g. gold (leaving him with less wealth for other gear), or the Leadership feat, the mount is also included in the NPC's CR.
If the mount is effectively a separate entity from the NPC, then its CR adds to that of the NPC.
If the NPC has the mount because of a class feature, the mount is included in the NPC's CR. This makes for some odd cases, like a 1st-level halfling druid mounted on a riding dog, but there is enough of a fudge factor in CR that it doesn't matter very much. If necessary, the DM can include an easier encounter in the same adventure to balance it out.
If the NPC has obtained the mount by spending other resources, e.g. gold (leaving him with less wealth for other gear), or the Leadership feat, the mount is also included in the NPC's CR.
If the mount is effectively a separate entity from the NPC, then its CR adds to that of the NPC.