Your son needs to learn to think of the words not as words but as a collection of sounds. Go back to phonic first principles, and consider how each letter or combination of letters might be pronounced. Remember that groups of letters can be split to turn one syllable into two, or one sound into two, and equally, letters can be joined together to turn two sounds or syllables into one.
Thus for 'reap':
'r' will only have one pronunciation at the beginning of a word
'e' could be pronounced by itself as /ee/ (as in feet) or /e/ (bed), (though /re/ is unlikely)
'a' could be pronounced by itself as /ae/ (fate) or /a/ (cat), or /ar/ (father)
'e' and 'a' could be combined as /ee/ (bead) or /e/ (head) or /ae/ (break)
'p' will only have one pronunciation, (unless it is followed by 'h')
so 'reap' could be pronounced a number of ways:
/reep/, /rep/ or /raep/
/re/ + something (unlikely, so move on to -)
/ree/ + /ap/, /ree/ + /aep/, or /ree/ + /arp/
Similarly 'pear' could be pronounced in a number of ways, depending on whether you split the vowels to make two sounds, or join them as one:
'p' will only have one possible pronunciation, since it is preceded by another p
If the vowels were separated, then 'e' could be as indicated above
in which case 'a' would combine with 'r' to give /ar/
or you could have 'e' and 'a' and 'r' in combination, which could give you /ee/+/r/ (hear) or /ae/+/r/ (pear)
So 'pear' could be
/pae/+/r/ (ie, 'pear', the fruit)
/pee/+/r/ (ie, 'peer', to look)
This is all a bit complicated to look at, but hopefully you get my drift. By seeing the word for the fruit 'pear', and not seeing a collection of letters with a bunch of different pronunciations, you get blinded to the other possibilities.
For an exposition of sounds and letter combinations, see 'Why children can't read' by Diane McGuinness (particularly the table 5.7 'Code Overlap' on page 107) and 'Reading Reflex' by Carmen McGuiness and Geoffrey McGuinness.
Best of luck