Several things to keep in mind when deciding the 'best' method of measuring an ID.
1) What is the tolerance of the feature?
2) What is the function of the feature?
3) What are you REALLY trying to determine (i.e. minimum diameter, maximum diameter, roundness, etc)
4) What does the customer need/want/expect?
I have used a variety of measuring equipment over the years, and find that anything that takes a discrete number of points (CMM, Shadowgraph, etc) will yield different results (sometimes significantly different) depending on which points you take, and how many. This is due to the software configuration for circle interpolation (least squares, best fit, etc)
A Sunnen gauge (and to lesser extent a bore micrometer) can be used to measure the entire diameter, and find the least diameter (but not always the greatest diameter, unless lobes are opposed by 120°). The Sunnen gauge has a further limitation of only checking to a very shallow depth.
The most common method that I use for verifiying diameter is a gauge pin. Most holes are designed to accept a mating component (bolt, shaft, etc) and you are generally interested in determining the minimum functional size of the hole.
Hope this is of some help.