When communicating altitude with a '9' in it, should it be pronounced "nine hundred" or "niner hundred"?
In the UK, the RT rules for the ANO are in Cap 413 and section 2.13.2 states:


  All numbers used in the transmission of altitude, height, cloud
  height, visibility and runway visual range information which contain
  whole hundreds and whole thousands shall be transmitted by pronouncing
  each digit in the number of hundreds or thousands followed by the word
  HUNDRED or TOUSAND as appropriate. Combinations of thousands and whole
  hundreds shall be transmitted by pronouncing each digit in the number
  of thousands followed by the word TOUSAND and the number of hundreds
  followed by the word HUNDRED; examples of this convention are as
  follows:

Table 5 
Number    Transmitted as              Pronounced as 
10        One Zero                    WUN ZERO
100       One Hundred                 WUN HUN DRED 
2 500     Two Thousand Five Hundred   TOO TOUSAND FIFE HUNDRED 
11 000    One One Thousand            WUN WUN TOUSAND 
25 000    Two Five Thousand           TOO FIFE TOUSAND



There isn't a specific example of NINER here, but given that the examples do actually use their prescribed pronounciations, you'd expect NINER to be used too. 

I can't remember hearing it but the other conventions seem to be adhered to by professional pilots in the UK (we Sunday afternoon bimblers are not as good at it).  Non-native english speakers are very exact in their use of the published pronounciation

No doubt there will be a professional along in a minute, who can give you a more authoritative answer

EDIT: The reason I can't remember hearing "Niner-thousand-niner-hundred" may be because, in the UK, it would be above the transition level?