Since you mentioned that what you are looking for is similar to "Journey to the Center of the Earth", did you happen to look the different versions of it. There are movies, mini-series, TV movies, etc. based upon Verne's novel.
Look at these movie connections here (and probably you also should a look at Verne's movie page, where it says which of his novels have been adapted):
http://www.imdb.com/board/10373051/movieconnections

Hmm, it could be "All That Glitters", you're right. I'll check it.

All That Glitters (1995)

Thanks, but it isn't. Rather tough to find.

Deep Rising
http://www.imdb.com/board/10118956/reference
otherwise, maybe Gulliver's Travels
http://www.imdb.com/board/11320261/reference

Thanks for guess, but it isn't. I added new info in main thread.

Just because they aren't on the list (I haven't seen them so I can't confirm I'm afraid), there are two purportedly pretty crummy pirate comedies from the 1980s that haven't been mentioned yet, and that ending sounds like something that might have been in either:
Yellowbeard (1983)
(the much more likely candidate, it's one of those silly comedies with fifty different stars)
Nate and Hayes (1983)
(probably not this one, but what the hey)

Thanks for list. I'll check it.

Maybe a look at this list might be helpful
http://www.thepirateking.com/movies/

Unfortunately, not yet. But I'll try to jog my memory.

I'm guessing none of the movies helped to jog your memory about other things that might help in finding the one you're looking for?
(Also, courtesy bump for you.)

I'll check it, but I didn't watch earlier this movie. However, thanks for guess.

It sounds vaguely like
Time bandits
. I believe there is a giant so big he wears a full sized ship on his head which rise out of the ocean when he comes to shallow water.

Take a look at this list https://en.m.wikipedia.org/wiki/List_of_pirate_films

Yeah there's no sea monster in The Goonies. There's a one eyed monster called willy though
.

I'm sure it won't be "The Goonies" even though I suggested it, but my hope is that something from it may remind you of something else that can help find the movie you are thinking about.

Unfortunately, it isn't any of them. I know "The Adventures of Baron Munchausen" and I'll check "A Kid in Aladdin's Palace" and "The Goonies" (because I didn't know).

Some ideas for you
A Kid in Aladdin's Palace (1997)
The Adventures of Baron Munchausen (1988)
The Goonies (1985)
Even if none of those are what you are looking for, does it help to remember any additional details?

You're right. It could be comedy film, perhaps pirates are only short theme. I give easy example:
"Mysterious Island" (1961)
is adventure movie, but there are pirates as well, although it isn't typical pirate movie.

The ending sounds like a comedy, but there aren't a whole lot of pirate comedies.
It's been a few years last time you were on this board. I thought you went through all the movies you couldn't remember.

It's very good guess, but I don't know why I remember (100%) sea monster. It could be something from 90's, because I remember better colours.

Probably not this one but TH3E SWISS FAMILY ROBINSON, 1960, features pirates; however I cannot recall any sea monster.

Unfortunately, it isn't.

Well there is also Pirates with Walter Matthau and The Pirate Movie, but they are both from the 80s.