I just noticed that there are two words which mean bookstore: der Buchladen and die Buchhandlung. Which of these two words is preferable? I'm using this in the context of "Ich gehe in die Buchhandlung (den Buchladen)."
In cases like yours, Google Ngrams gives you a good start.
You can clearly see that Buchhandlung is by far the most frequently used variety to describe stores selling books.
While in a more colloquial context a "Buch-" or "Bücherladen" will be both used and understood, "Buchhandlung" is correct in every register.
Buchladen is the word that I would use in most cases, while Buchhandlung sounds more technical to me. Some of the other answers here let me suspect that there are regional differences, I am from Berlin.
As an example, I have found a list of zehn tolle Buchläden in Berlin. There you see both words being used and also book stores having Buchhandlung or Buchladen in their name.
Looking at some other examples, it seems that Buchladen evokes the image of a smaller store.
Buchhandung is definitive preferable. Buchladen is nowhere near as idiomatic.
Laden is a colloquial term and you can make up all kind of -läden. People even call the place you can get doner kebab Dönerladen. Laden can also carry negative connotations: A Saftladen, for instance, is not a place where you can buy juice, but used to refer to any institution that provides bad service or bad products or is otherwise just not recommendable.
Buchladen? A Laden for books? No, no! Laden sounds like wild consumerism, but books that's the true, the beautiful and the good.
A Handlung on the other hand clearly feels like competence and seriousness. A book that is something of importance by itself, something that most be respected and honoured unlike eggs and cloths and therefore needs a proper Handlung instead of a Laden! It's a Kulturgut.
I clearly exaggerate here, but I belive that this idea somehow unspoken is in the mind of the average german or at least many germans. You can use Buchladen or idmean's Buchgeschäft e.g. in novels if you don't want to use Buchhandlung over and over again but in everyday German Buchhandlung is the common used word.