Both are correct
Drake companions gain 6 + int modifier skill ranks per HD.
However, the table already takes into consideration the Starting Statistics of a drake companion, listed on the following page:
Drake Starting Statistics
Size Tiny; Alignment any nongood; Speed 20 ft.; Attack bite
(1d3), tail* (1d3); Ability Scores Str 8, Dex 17, Con 11, Int 4,
Wis 10, Cha 7; Languages Draconic. *This is a secondary
natural attack; see page 182 of the Pathfinder RPG Core Rulebook
for more information on how secondary attacks work.
As we know, a creature with 4 int has a -3 int modifier, and thus they gain 3 skill ranks per HD due to that penalty. If you happen to increase the companion's int score to 6 (possibly at 10th level), this modifier also changes and they would, instead, gain 4 skill ranks per HD.
There is an error on the table, however, when the ranks increase even when the companion HD does not, unlike it happens on the druid's animal companion table. The companion should not gain skill ranks when they do not gain HD. You will notice that feat's follow the standard rules and they gain one new feat every odd HD (3, 5, 7, etc).