Scanner and BufferedReader technically aren't InputStreams (at least not java.io.InputStream)
They are both classes that utilise them though, so I'll read the question in that you are discussing different ways of handling input.
Looking at the API for these classes:
Buffered Reader: Reads text from a character-input stream, buffering characters so as to provide for the efficient reading of characters, arrays, and lines.
Scanner: A simple text scanner which can parse primitive types and strings using regular expressions.
So if I you want to read in big lump of text then BufferedReader seems appropriate.
If you want to interpret and parse it in a smarter manner, maybe the Scanner is what you are after.
You could still use BufferedReader to read the input line by line, and do
string operations on that rather than using the scanner. In fact that's what many people were doing before the Scanner came along in Java5 (and some are probably still doing regardless)
Is it wrong to use the BufferedReader in that scenario? - I don't think so. So long as it works.
Is it more complicated than the Scanner equivalent? Possibly. If it can be expressed in regular expressions, then the Scanner may be easier to code/more efficient. But then maybe not too if you have some massively weird processing.
In general: Read the API, understand the classes, and use them in the appropriate scenario.
That is where your judgement has to come into play. There is never just one answer, and people will debate over which may be the 'best' answer.
You have to consider things like amount of effort required, readability, flexibility of code etc etc.
Welcome to the wonderful world of programming.