The article "Research on TM and Other Forms of Meditation Stinks" highlights some of the flaws in meditation research. An important point to be made is the difficulty of precisely defining meditation itself.
Even more difficult would be capturing details of brief, spontaneous peak experiences.
My sense is that we are slowly getting better at this, with some of the older research being more of a stone knives and bearskins kind of thing. Many people are aware that private research funded by a group with an agenda (such as Transcendental Meditation) may not constitute the highest expression of reasonable investigation.