A manager in our company (not really familiar with RACI) insists on having task "Work estimation" in the RACI. I am not really sure but IMHO it does not belong here as it is included in the activities..but I cannot justify. Should be there or not..and if not, how can I explain?
The RACI matrix itself is not the point. The need to have "work estimation" in the matrix is inherent in a major stakeholder requiring the information the RACI matrix provides. In other words, the manager wants to know, or assign, key resources that must be involved in estimating work, either as an R, A, C, or I. Therefore, implicit in the manager's want, it needs to be in there.
The primary purpose of a RACI matrix is to clarify who does what. If there is any opportunity for misunderstanding or misinterpretation, then get it clarified in the matrix.
Part of this may come down to the level of granularity in the matrix: too high a level and you won't be able to say with certainty where certain responsibilities lie. Too low a level, and you run the risk of having to cover every single eventuality in detail. I work in IT, and I would not consider including something like "Build Unix server" as a separate task from "Build Windows Server". Even although both of these are different, and done by different teams, I would keep this as "Build server" and state the responsibility as being the "technical specialist". But I would separate out "build server" from "specify server", and also from "configure storage".
Relating this to your question, I would expect that, depending on your place of work, estimating work could be done by a project manager, an estimator, a designer, a team leader, or a technical specialist. If there is any lack of clarity - and it seems that there might be - then don't worry about convention. Put it into the matrix, and remove the doubt.
I'm not entirely sure what "work estimation is", but I've never included it in any RACI I've created. @DavidEspina has interpreted the term differently than I would have, and if you accept his interpretation of this term, then his answer is probably correct. On the other hand, if I were to interpret the term, I would assume that "work estimation" was "estimated duration", then I would strongly advise against this, and work with the manager to establish that the project planning will include both the RACI and the estimated duration, but these will not occur in the same product (except in the case that the Project Management Plan will reference all project documentation).
RACI should emphasize cooperation between the stakeholders - who is Responsible Accountable, Consulted and Informed about decisions and work products. RACI is an aid to governance, not part of the project planning process. The PMBOK is largely silent on governance; different organizations will handle it differently. In my experience you need an initial governance process in the project charter/project initiation documentation, and frequently the RACI is at least outlined during this process group.
Estimated Duration is essential to project planning. Estimated duration is developed after the Work Breakdown Structure and WBS Dictionary. (Many Project Initiation Documents do provide a high level estimate of the work, but that is usually a Rough Order of Magnitude estimate accurate to +/- 80%.)
Trying to incorporate estimated duration in the RACI would require that the RACI be completed at the same time as the WBS & Project Schedule; deferring governance to the project planning stage will seriously damage the project and may result in project failure.
Perhaps more seriously, estimated duration can change (should change) as the project progresses. You'll have better information to refine your estimates. Change management for the schedule is difficult; I don't want to do change management on the RACI. The RACI should change very rarely (like most project initiation documents).
If the manager merely wants to label who is responsible for estimating the work, then you have a different problem. The project team is always responsible for estimating the work. If the manager wants to assign that responsibility to any entity other than the project team, then I would highly recommend seeking a new position because that project is doomed to failure.