there are no official canon books, the only canon materials are the television shows and movies
I usually consider the books to be canon.
The controversy around the books will probably never go away, but here's the breakdown.
The original books were liscenced to third parties (Whitman Books, Bantam Books) to be written independently of any review by Paramount or CBS (which were then seperately managed and possibly seperately owned (someone fill in that detail possibly). This led to many inaccuracies and contradictions, so that the books had to listed as non-canon in order not to disrupt the continuity of the Star Trek universe. However, sometime after that, the books began to be published 'in-house' so to speak, by Simon and Schuster, a publishing company owned by CBS. These later books were written to be a cohesive universe, and CBS keeps a close watch on them. There are many fewer continuity issues with these books, and although not considered canon by many, plot points in the books have actually been used as the basis for later plot points in TNG, DS9, VOY, and ENT, leading many to consider them as 'soft canon'.