Two goals from Greece international Stelios Giannakopoulos, an overhead kick from Gary Speed and a late strike from substitute Henrik Pedersen secured the points for Sam Allardyce's men.
Former England international Teddy Sheringham pulled a goal back for the visitors, but his late effort was scant consolation.
Trailing 3-0 at the break West Ham were always going to find it hard to mount a comeback, but with Sheringham's goal they had a glimmer of light.
Their hopes were ended within two minutes, however, when Pedersen restored the three-goal cushion in the 81st minute and Allardyce's men continued their charge for a European place.
Ricardo Vaz Te jumped tallest in the 12th minute as Bolton took an early lead
The Portuguese's header fell perfectly into the path of Stelios and after the ball rebounded off the foot of the post it was a simple tap-in from close range.
It could have been 2-0 to the home side just three minutes later, but Jay-Jay Okocha's fierce shot was blocked by Hayden Mullins.
Earlier, Lionel Scaloni fired wide from 25 yards for the visitors, who then had another good chance in the 24th minute, but Shaun Newton's shot was blocked and cleared by Bolton full-back Joey O'Brien.
In the 29th minute Ricardo Gardner went agonisingly close with a powerful left-foot shot which flew over the bar.
Four minutes later Bolton doubled their advantage when Nolan crossed from the right for Stelios and the in-form 31-year-old grabbed his second goal of the game.
It was an easy close-range finish, but it was well taken all the same.
Stelios then had a glorious chance to grab his hat-trick, but his curling left-foot shot went inches over the crossbar as Bolton continued to dominate.
In the 42nd minute midfielder Speed drilled a left-foot shot just over the bar, but three minutes later had a big smile on his face.
The ex-Wales captain jumped athletically on the stroke of half-time to meet a Gardner cross with an overhead kick which flew into the back of the net.
Bolton were coasting at the break.
A minute after the re-start Kevin Nolan saw a volley blocked by Anton Ferdinand, before at the other end Yossi Benayoun forced Bolton keeper Jussi Jaaskelainen to make a smart stop.
In the 53rd minute Stelios, still searching for his hat-trick, fired wide of the left post, before Speed shot wide three minutes later.
West Ham kept battling and Mullins fired wide before Bobby Zamora had a left-foot shot blocked by Radhi Jaidi.
Christian Dailly then fired wide of the right hand post, before the pressure eventually told.
In the 78th minute, Jaaskelainen could only parry a shot from Benayoun and Sheringham could not miss from close range.
West Ham's joy soon turned sour when Pedersen, having only been on the pitch for a few minutes, found time and space to fire past visiting goalkeeper Shaka Hislop with a clinical left-foot strike.
Sheringham could have made it 4-2 in the last minute but shot wide with a left-foot shot and West Ham were left to pick up the pieces.