Dataset and Fileset are almost the same . 

Dataset is tool dependent and File Set is OS dependent(UNIX).
Dataset don't have any regulation of the amount of data that it has where as Fileset have limits to the data.

just want to add something to the previous answer

Data sets are operating system files,
 each referred to by a control file, which by 
convention has the suffix .ds. 
The control file points IBM InfoSphere DataStage 
to a set of other files that carry the data. 
The location of these data files is determined by the “resource disk” property in the configuration file used to run the job. Using data sets wisely can be key to good performance in a set of linked jobs. 
You can also manage data sets independently of a job using the Data Set Management utility, available from 
the IBM InfoSphere DataStage and QualityStage Designer or Director.

WebSphere  DataStage  can  generate  and  name  exported  files,  write  them  to  their destination,  and  list  the  files  it  has  generated  in  a  file  whose  extension  is,by  convention,.fs.The data files  and  the  file  that  lists  them  are  called  a  file  set.This  capability  is  useful  because  some  operating systems  impose  a  2  GB  limit on the size of a file and you need to distribute  files among nodes to prevent overruns. The amount of data  that can be stored in each destination  data  file  is  limited by the characteristics of the file system and the  amount of free disk space available.